At eight years old, Michele went with a friend to an open casting call for a musical. She decided on a whim she wanted to try out. She was offered the part and made her debut on Broadway in 1995 as a replacement in the role of Young Cosette in the New York City showing of Les Misérables. Then, in 1998, she played Tateh's daughter, the Little Girl, in the original Broadway cast of Ragtime. In 2004, Michele played Shprintze and Chava in the Broadway revival of the musical Fiddler on the Roof. She also sang on the 2003 Broadway revival cast recording of Fiddler on the Roof.

She played the role of Wendla in Steven Sater and Duncan Sheik's musical version of Spring Awakening, starring in early workshops to Off-Broadway and finally playing the role in the Broadway production at the age of 20.[9] Around the same time that the show was set to go to Broadway, she was offered the role of Eponine in the Broadway revival of Les Misérables.[10] She decided to remain with Spring Awakening, which debuted on Broadway in December 2006. She was nominated for a Drama Desk Award for her acting in Spring Awakening in the category of Outstanding Actress in a Musical.[11]

On May 18, 2008, Michele left Spring Awakening with co-star Jonathan Groff. She acted in a reading of Sheik and Sater's new musical, Nero, in July 2008 at Vassar College.[12] From August 8–August 10, 2008, she played Eponine in the Hollywood Bowl's Les Misérables concert. She sings on the original Broadway cast recordings of Ragtime and Spring Awakening.

Michele is active in charities for gay rights and animal rights, as well as in numerous other charities. In 2008, Michele was a part of the PETA ad campaign "Buck Cruelty! Say No to Horse-Drawn Carriage Rides".[23] In April 2010, Michele appeared in a PSA for PETA speaking out against fur clothing.[24] In September 2010, Michele was honored by PETA for her work for animals.[25] In addition to working with PETA, Michele is also a vegan.[26]

In 2008, Michele performed at a benefit concert, "Alive in the World",[30] to aid the Twin Tower Orphan Fund. Michele has also been active with Broadway Cares/Equity Fights AIDS. For Broadway Cares, Michele has participated in Broadway Barks, Broadway Bares, Easter Bonnet Competition and The Flea Market and Grand Auction. In October 2010, Michele performed at a benefit concert for the Painted Turtle, a camp for children with illnesses. The concert celebrated the 35th anniversary of The Rocky Horror Picture Show, with Michele playing the lead role of Janet Weiss for the benefit.[31] In February 2011 she performed for The Grammy's MusiCares Benefit in Los Angeles, California. Money earned by the event go to help musicians in need.[32]